Welcome to the Wicked Edge Forum, Jon. I’ll try to help you with addressing each issue.
The indexing on the square bar are intended only to be an indicator of your gross angle settings. Theses indicators were originally calibrated, I believe using a knife with it’s edge horizontally clamped 5/8" above the vise’s jaws line. Any difference in how a knife is mounted will effect the angle cube readings vs the indexes. The beauty and the precision of the W.E. sharpeners are they allow a large variety of knives of various sizes, shapes and designs to be clamped in a variety of positions that best suit the individual knives as we set the relative bevel angles allowing us to profile and sharpen the knives repeatedly at that same desired relative angle setting. A properly zeroed digital angle device is the truest measure of your relative angles. I use the term “relative angle” because the angle reading is realtive to the W.E. sharpener and the surface it’s resting on. Zeroing the angle cube on the stationary resting W.E. sharpener allows us to set the sharpening angles relative to the sharpener as it sits.
The W.E. sharpeners can sharpen a very wide range of knives at a range of sharpening angles. The narrowest limits of these bevel angles are determined by the height of the knife edge above the jawline. With a narrow knife at low angles the sharpening stones may contact the vise or jaws inhibiting the ability to sharpen the knife. This is the situation you found requiring you to use the low angle adapter, (LAA). Even using the LAA the knife may still be too narrow and too low to sharpen without stone< >vise conflict. You may try to adjust the clamped knife so it is held higher in the LAA, held just by the tips of it’s adapter clamp. Even still this may not work.
The next recommended option is to try a “Tormek Small knife Holder”. This adapter holds the knife by the handle out in front of the W.E. vise. Between the LAA and the Tormek, I’ve been able to sharpen most knives. The LAA and Tormek do make it difficult to record your sharpening clamping settings for repeating when doing touch-ups . (Another issue to learn how to deal with).
Be aware, the LAA does offset the clamped knife to one side by the nature of the adapter’s design. The LAA’s stationary side is clamped in the W.E. jaws so the knife is held off to one side above the outside of the vise jaws. Because of the LAA’s design and clamping position the gross angle indexing on square bar will then be very different from side to side. I believe this is where you saw that big variance. By comparing the knife’s angle clamped in just the W.E. vise jaws, first, and comparing these angle readings to the angles measured after reclamping that same knife in the LAA it may provide you with a basis for comparison to use to adjust your relative angle settings to compensate for the shift in the clamping position while using the LAA.
Last thing, when profiling your knife to your relative angle while drawing a burr, as you learned, after spending some time and effort to draw the burr to the first knife side, that it only takes a little more effort to the other knife side to then flip that burr back over. Then the first bevel is much taller then the second side’s bevel. You can continue to work to remove more steel from the second side bevel to even out the heights, from side to side.
I prefer to scrub only a small amount on the first side then alternate to the second side. Then scrub on the second side, then swap again. Alternating back and forth, side to side, I develop both bevels at the same time while attempting to keep the bevels equal height from the start. This method allows me to limit steel waste because I can stop as soon as the burrs are formed on both sides. It allows me to avoid chasing the burr as it flips back and forth from side to side or messing with the bevel heights from side to side to get them evened out.
Realize all these tips are easier said then done. From your questions it sounds as though you are right where you should be after only 5 knives. It takes time. The best tip I can share is go slow and compare knife side to side looking at the results of your actions and what your sharpening strokes do. When you can correlate your actions and results you’ll know what you’re doing and how to get it done.